Abstract

Human settlement of the Japanese archipelago is of significant interest for understanding how human populations migrated from
the East Asian continent to isolated islands and shifted lifestyles from hunter‐gathering to farming. The hunter‐gathering
Jomon period follows the Palaeolithic period but precedes the agricultural Yayoi period. Three hypotheses have been proposed
to model the population history in the Japanese archipelago. Two of these are in contrast with each other, hypothesising that
lineages leading to modern Japanese are traced back to a single ancestor of indigenous Jomon (the transformation hypothesis)
or migrant Yayoi (the replacement hypothesis) people. The third model postulates a hybridisation lineage or an admixture of
the two ancestral populations. Recent advances in high‐throughput technology have enabled the application of genome‐scale
data to directly test the three models. Several lines of population genetics studies strongly support the hybridisation hypothesis
to explain the origin of modern Japanese.

Key Concepts

Prehistory in the Japanese archipelago is characterised by the Jomon and Yayoi cultures.

A major cultural transition from the Jomon period to the Yayoi period is a shift in lifestyles from hunter‐gathering to farming.

Three demographic models have been proposed to explain the origin of modern Japanese: transformation, replacement and hybridisation.

A dual structure hypothesis is based on the hybridisation model and assumes that modern Japanese is admixed between the indigenous
Jomon and migrated Yayoi people, and the degree of admixture varies among local populations in the Japanese archipelago.

Population genetics analyses have been performed to make inferences about the evolutionary history of modern Japanese.

Genomic data, as well as genetic data from a single locus or small number of loci, support the hybridisation hypothesis to
explain the origin of modern Japanese.

Statistical modelling based on genomic data shows a complex history characterised with the population stratification of the
Jomon people in the Japanese archipelago.

Figure 1. Cultural transition in the Japanese archipelago and three hypotheses on the origin of modern Japanese. The Jomon culture started around 13 000 years ago (13 kya). The Japanese archipelago consists of five major islands including Hokkaido, mainland Japan, Shikoku, Kyushu and Okinawa. The Jomon people widely spread through the islands. Then, the transition occurred around 3 kya when the Yayoi culture migrated through the Korean Peninsula. The main question is how people living during the Jomon or Yayoi period contributed to the formation of modern Japanese. Three hypotheses have been proposed: the transformation, replacement and hybridisation models.

Figure 2. Testing three hypotheses for the origin of modern Japanese by formulating three models using genome‐scale data from three populations. Ainu or Han Chinese in Beijing (CHB) is assumed as direct descendants from the Jomon or Yayoi lineages, respectively. Japanese from Tokyo (JPT) represent modern Japanese. The transformation model does not involve demic diffusion during the spread of the Yayoi culture; therefore, the lineage leading to JPT split from the shared ancestor with the Ainu. By contrast, the replacement model postulates that JPT are descendants of the Yayoi people, so the JPT lineage branches off from the Yayoi lineage. The hybridisation model postulates admixture between the Jomon and Yayoi lineages, so that both of the ancestors contribute to the formation of JPT.

Figure 3. Complex demography inferred from genome‐wide SNP data. The model is essentially the same as the hybridisation model (Figure), but this model includes divergence in the Jomon lineages that occurred after the split between the Jomon and Yayoi lineages but before admixture. One lineage leads to contemporary Ainu living in Hokkaido, whereas the other contributes to the admixture with the Yayoi people. The change in recent migration rates is shown as a thick arrow.

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